Supplementary files for the SPPI preprint: A transparent multicriteria and fuzzy classification approach for genome-based probiotic candidate prioritisation

This record contains the supplementary files associated with the preprint entitled “A transparent multicriteria and fuzzy classification approach for genome-based probiotic candidate prioritisation”. The deposited archive provides the datasets, analysis outputs, figures, scripts, and execution logs used to support the development and evaluation of SPPI, a genome-based multicriteria framework for probiotic candidate prioritisation. The files are provided to support transparency, traceability, and reproducibility of the analyses reported in the preprint. The archive is organised as follows: 00_README: README file describing the organisation and content of the supplementary repository. 01_AHP_Expert_Recruitment: anonymised AHP expert recruitment and response summary, including the national, international, and Scopus-derived expert groups used to document the contacted/referred expert pool. 02_AHP_Calculator_V7: AHP calculator files, anonymised questionnaire-response materials, pairwise-comparison analysis outputs, consistency-ratio results, retained expert matrices, AHP-derived weights, and equation outputs used to establish the weighting structure. 03_Curated_Genome_Dataset: curated 48-genome dataset metadata and associated ProbML outputs used for post-classification comparison on the same genome dataset. 04_Probiogenomic_Screening_Results: consolidated outputs from the modular probiogenomic screening pipeline, including genome-by-feature matrices, feature catalogues, module summaries, marker-level outputs, and screening result summaries. 05_Mapping_and_Subpillar_Distributions: mapping files and marker/subpillar presence-absence matrices used to connect detected genomic markers with functional categories and SPPI subpillars. 06_SPPI_Scoring: retained SPPI Iteration 2.8 scoring files, including scoring inputs, mapping files, equations, scripts, genome-level scores, ranking outputs, group-level analyses, and associated analysis outputs. 07_FCE_Classification: FCE classification outputs associated with SPPI Iteration 2.8, including Iteration 7.0 classification results, confidence summaries, confusion-matrix outputs, sentinel-genome audit files, and post-classification comparison with ProbML. 08_Figures: main preprint figures and supplementary figures supporting AHP weighting, genome-wide feature analysis, curated-marker analysis, SPPI scoring, and FCE classification. 09_Scripts: source scripts and execution logs associated with AHP weighting, the probiogenomic screening pipeline, marker-level statistical analyses, genome-wide multivariate analyses, SPPI scoring, FCE classification, and figure generation. Some files are intentionally present in more than one location to preserve step-level reproducibility. Major analytical sections retain their required inputs, scripts, mapping files, intermediate outputs, and final outputs so that each workflow component can be interpreted independently. These repeated files represent controlled copies preserving the computational context of each analysis step and should not be interpreted as alternative versions or independent datasets.